+++ /dev/null
-/*
- * consensusseqscommand.cpp
- * Mothur
- *
- * Created by westcott on 11/23/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "consensusseqscommand.h"
-#include "sequence.hpp"
-#include "inputdata.h"
-
-//**********************************************************************************************************************
-vector<string> ConsensusSeqsCommand::setParameters(){
- try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pcutoff("cutoff", "Number", "", "100", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-
- vector<string> myArray;
- for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string ConsensusSeqsCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The consensus.seqs command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.\n";
- helpString += "The consensus.seqs command parameters are fasta, list, name, cutoff and label.\n";
- helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required, unless you have a valid current fasta file. \n";
- helpString += "The list parameter allows you to enter a your list file. \n";
- helpString += "The name parameter allows you to enter a names file associated with the fasta file. \n";
- helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
- helpString += "The cutoff parameter allows you set a percentage of sequences that support the base. For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences.\n";
- helpString += "The consensus.seqs command should be in the following format: \n";
- helpString += "consensus.seqs(fasta=yourFastaFile, list=yourListFile) \n";
- helpString += "Example: consensus.seqs(fasta=abrecovery.align, list=abrecovery.fn.list) \n";
- helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "getHelpString");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-ConsensusSeqsCommand::ConsensusSeqsCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- outputTypes["summary"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
- exit(1);
- }
-}
-//***************************************************************************************************************
-ConsensusSeqsCommand::ConsensusSeqsCommand(string option) {
- try {
- abort = false; calledHelp = false;
- allLines = 1;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
-
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
-
- ValidParameters validParameter;
- map<string,string>::iterator it;
-
- //check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- outputTypes["summary"] = tempOutNames;
-
-
- //if the user changes the input directory command factory will send this info to us in the output parameter
- string inputDir = validParameter.validFile(parameters, "inputdir", false);
- if (inputDir == "not found"){ inputDir = ""; }
- else {
- string path;
- it = parameters.find("fasta");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["fasta"] = inputDir + it->second; }
- }
-
- it = parameters.find("name");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["name"] = inputDir + it->second; }
- }
-
- it = parameters.find("list");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["list"] = inputDir + it->second; }
- }
- }
-
-
- //check for parameters
- fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") {
- fastafile = m->getFastaFile();
- if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setFastaFile(fastafile); }
-
- namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { namefile = ""; abort = true; }
- else if (namefile == "not found") { namefile = ""; }
- else { m->setNameFile(namefile); }
-
- listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not open") { abort = true; }
- else if (listfile == "not found") { listfile = ""; }
- else { m->setListFile(listfile); }
-
- label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; }
- else {
- if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
-
- string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "100"; }
- m->mothurConvert(temp, cutoff);
-
- //if the user changes the output directory command factory will send this info to us in the output parameter
- outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
-
- if (namefile == ""){
- vector<string> files; files.push_back(fastafile);
- parser.getNameFile(files);
- }
- }
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
-int ConsensusSeqsCommand::execute(){
- try{
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- readFasta();
-
- if (m->control_pressed) { return 0; }
-
- if (namefile != "") { readNames(); }
-
- if (m->control_pressed) { return 0; }
-
-
- if (listfile == "") {
-
- ofstream outSummary;
- string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.summary";
- m->openOutputFile(outputSummaryFile, outSummary);
- outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
- outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
-
- outSummary << "PositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
-
- ofstream outFasta;
- string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.fasta";
- m->openOutputFile(outputFastaFile, outFasta);
- outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
-
- vector<string> seqs;
- int seqLength = 0;
- for (map<string, string>::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
-
- if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- string seq = fastaMap[it->second];
- seqs.push_back(seq);
-
- if (seqLength == 0) { seqLength = seq.length(); }
- else if (seqLength != seq.length()) { m->mothurOut("[ERROR]: sequence are not the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
-
- }
-
- vector< vector<float> > percentages; percentages.resize(5);
- for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
-
- string consSeq = "";
- //get counts
- for (int j = 0; j < seqLength; j++) {
-
- if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
- int numDots = 0;
-
- for (int i = 0; i < seqs.size(); i++) {
-
- if (seqs[i][j] == '.') { numDots++; }
-
- char base = toupper(seqs[i][j]);
- if (base == 'A') { counts[0]++; }
- else if (base == 'T') { counts[1]++; }
- else if (base == 'G') { counts[2]++; }
- else if (base == 'C') { counts[3]++; }
- else { counts[4]++; }
- }
-
- char conBase = '.';
- if (numDots != seqs.size()) { conBase = getBase(counts, seqs.size()); }
-
- consSeq += conBase;
-
- percentages[0][j] = counts[0] / (float) seqs.size();
- percentages[1][j] = counts[1] / (float) seqs.size();
- percentages[2][j] = counts[2] / (float) seqs.size();
- percentages[3][j] = counts[3] / (float) seqs.size();
- percentages[4][j] = counts[4] / (float) seqs.size();
-
- }
-
- for (int j = 0; j < seqLength; j++) {
- outSummary << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << seqs.size() << '\t' << consSeq[j] << endl;
- }
-
-
- outFasta << ">conseq" << endl << consSeq << endl;
-
- outSummary.close(); outFasta.close();
-
-
- }else {
-
-
- InputData* input = new InputData(listfile, "list");
- ListVector* list = input->getListVector();
-
- string lastLabel = list->getLabel();
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete list; delete input; return 0; }
-
- if(allLines == 1 || labels.count(list->getLabel()) == 1){
-
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
-
- processList(list);
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
- }
-
- if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = list->getLabel();
-
- delete list;
-
- list = input->getListVector(lastLabel);
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
-
- processList(list);
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
-
- //restore real lastlabel to save below
- list->setLabel(saveLabel);
- }
-
- lastLabel = list->getLabel();
-
- delete list; list = NULL;
-
- //get next line to process
- list = input->getListVector();
- }
-
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } if (list != NULL) { delete list; } delete input; return 0; }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- if (list != NULL) { delete list; }
-
- list = input->getListVector(lastLabel);
-
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
-
- processList(list);
-
- delete list; list = NULL;
- }
-
- if (list != NULL) { delete list; }
- delete input;
- }
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
- m->mothurOutEndLine();
-
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "execute");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
-int ConsensusSeqsCommand::processList(ListVector*& list){
- try{
-
- ofstream outSummary;
- string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.summary";
- m->openOutputFile(outputSummaryFile, outSummary);
- outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
- outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
-
- ofstream outName;
- string outputNameFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.names";
- m->openOutputFile(outputNameFile, outName);
- outputNames.push_back(outputNameFile); outputTypes["name"].push_back(outputNameFile);
-
- ofstream outFasta;
- string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.fasta";
- m->openOutputFile(outputFastaFile, outFasta);
- outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
-
- outSummary << "OTU#\tPositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
-
- for (int i = 0; i < list->getNumBins(); i++) {
-
- if (m->control_pressed) { outSummary.close(); outName.close(); outFasta.close(); return 0; }
-
- string bin = list->get(i);
-
- string newName = "";
- string consSeq = getConsSeq(bin, outSummary, newName, i);
-
- outFasta << ">seq" << (i+1) << endl << consSeq << endl;
- outName << "seq" << (i+1) << '\t' << "seq" << (i+1) << "," << newName << endl;
- }
-
- outSummary.close(); outName.close(); outFasta.close();
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "processList");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-//made this smart enough to owrk with unique or non unique list file
-string ConsensusSeqsCommand::getConsSeq(string bin, ofstream& outSummary, string& name, int binNumber){
- try{
-
- string consSeq = "";
- bool error = false;
-
- //the whole bin is the second column if no names file, otherwise build it
- name = bin;
- if (namefile != "") { name = ""; }
-
- vector<string> binNames;
- m->splitAtComma(bin, binNames);
-
- //get sequence strings for each name in the bin
- vector<string> seqs;
-
- set<string> addedAlready;
- int seqLength = 0;
- for (int i = 0; i < binNames.size(); i++) {
-
- map<string, string>::iterator it;
-
- it = nameMap.find(binNames[i]);
- if (it == nameMap.end()) {
- if (namefile == "") { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta file, please correct."); m->mothurOutEndLine(); error = true; }
- else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta or name file, please correct."); m->mothurOutEndLine(); error = true; }
- break;
- }else {
-
- //add sequence string to seqs vector to process below
- string seq = fastaMap[it->second];
- seqs.push_back(seq);
-
- if (seqLength == 0) { seqLength = seq.length(); }
- else if (seqLength != seq.length()) { m->mothurOut("[ERROR]: sequence are not the same length, please correct."); m->mothurOutEndLine(); error = true; break; }
-
- if (namefile != "") {
- //did we add this line from name file already?
- if (addedAlready.count(it->second) == 0) {
- name += "," + nameFileMap[it->second];
- addedAlready.insert(it->second);
- }
- }
-
- }
- }
-
- if (error) { m->control_pressed = true; return consSeq; }
-
- if (namefile != "") { name = name.substr(1); }
-
- vector< vector<float> > percentages; percentages.resize(5);
- for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
-
- //get counts
- for (int j = 0; j < seqLength; j++) {
-
- if (m->control_pressed) { return consSeq; }
-
- vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
- int numDots = 0;
-
- for (int i = 0; i < seqs.size(); i++) {
-
- if (seqs[i][j] == '.') { numDots++; }
-
- char base = toupper(seqs[i][j]);
- if (base == 'A') { counts[0]++; }
- else if (base == 'T') { counts[1]++; }
- else if (base == 'G') { counts[2]++; }
- else if (base == 'C') { counts[3]++; }
- else { counts[4]++; }
- }
-
- char conBase = '.';
- if (numDots != seqs.size()) { conBase = getBase(counts, seqs.size()); }
-
- consSeq += conBase;
-
- percentages[0][j] = counts[0] / (float) seqs.size();
- percentages[1][j] = counts[1] / (float) seqs.size();
- percentages[2][j] = counts[2] / (float) seqs.size();
- percentages[3][j] = counts[3] / (float) seqs.size();
- percentages[4][j] = counts[4] / (float) seqs.size();
-
- }
-
- for (int j = 0; j < seqLength; j++) {
- outSummary << (binNumber + 1) << '\t' << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << seqs.size() << '\t' << consSeq[j] << endl;
- }
-
- return consSeq;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "getConsSeq");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
-char ConsensusSeqsCommand::getBase(vector<int> counts, int size){ //A,T,G,C,Gap
- try{
- /* A = adenine
- * C = cytosine
- * G = guanine
- * T = thymine
- * R = G A (purine)
- * Y = T C (pyrimidine)
- * K = G T (keto)
- * M = A C (amino)
- * S = G C (strong bonds)
- * W = A T (weak bonds)
- * B = G T C (all but A)
- * D = G A T (all but C)
- * H = A C T (all but G)
- * V = G C A (all but T)
- * N = A G C T (any) */
-
- char conBase = 'N';
-
- //zero out counts that don't make the cutoff
- float percentage = (100.0 - cutoff) / 100.0;
- int zeroCutoff = percentage * size;
-
- for (int i = 0; i < counts.size(); i++) {
- if (counts[i] < zeroCutoff) { counts[i] = 0; }
- }
-
- //any
- if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'n'; }
- //any no gap
- else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'N'; }
- //all but T
- else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'v'; }
- //all but T no gap
- else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'V'; }
- //all but G
- else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'h'; }
- //all but G no gap
- else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'H'; }
- //all but C
- else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'd'; }
- //all but C no gap
- else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'D'; }
- //all but A
- else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'b'; }
- //all but A no gap
- else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'B'; }
- //W = A T (weak bonds)
- else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'w'; }
- //W = A T (weak bonds) no gap
- else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'W'; }
- //S = G C (strong bonds)
- else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 's'; }
- //S = G C (strong bonds) no gap
- else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'S'; }
- //M = A C (amino)
- else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'm'; }
- //M = A C (amino) no gap
- else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'M'; }
- //K = G T (keto)
- else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'k'; }
- //K = G T (keto) no gap
- else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'K'; }
- //Y = T C (pyrimidine)
- else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'y'; }
- //Y = T C (pyrimidine) no gap
- else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'Y'; }
- //R = G A (purine)
- else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'r'; }
- //R = G A (purine) no gap
- else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'R'; }
- //only A
- else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'a'; }
- //only A no gap
- else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'A'; }
- //only T
- else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 't'; }
- //only T no gap
- else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'T'; }
- //only G
- else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'g'; }
- //only G no gap
- else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'G'; }
- //only C
- else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'c'; }
- //only C no gap
- else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'C'; }
- //only gap
- else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = '-'; }
- //cutoff removed all counts
- else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'N'; }
- else{ m->mothurOut("[ERROR]: cannot find consensus base."); m->mothurOutEndLine(); }
-
- return conBase;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "getBase");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-
-int ConsensusSeqsCommand::readFasta(){
- try{
-
- ifstream in;
- m->openInputFile(fastafile, in);
-
- while (!in.eof()) {
-
- if (m->control_pressed) { break; }
-
- Sequence seq(in); m->gobble(in);
- string name = seq.getName();
-
- if (name != "") {
- fastaMap[name] = seq.getAligned();
- nameMap[name] = name; //set nameMap incase no names file
- nameFileMap[name] = name;
- }
- }
-
- in.close();
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "readFasta");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
-int ConsensusSeqsCommand::readNames(){
- try{
-
- ifstream in;
- m->openInputFile(namefile, in);
-
- string thisname, repnames;
- map<string, string>::iterator it;
-
- bool error = false;
-
- while(!in.eof()){
-
- if (m->control_pressed) { break; }
-
- in >> thisname; m->gobble(in); //read from first column
- in >> repnames; //read from second column
-
- it = nameMap.find(thisname);
- if (it != nameMap.end()) { //then this sequence was in the fastafile
-
- vector<string> splitRepNames;
- m->splitAtComma(repnames, splitRepNames);
-
- nameFileMap[thisname] = repnames; //for later when outputting the new namesFile if the list file is unique
- for (int i = 0; i < splitRepNames.size(); i++) { nameMap[splitRepNames[i]] = thisname; }
-
- }else{ m->mothurOut("[ERROR]: " + thisname + " is not in the fasta file, please correct."); m->mothurOutEndLine(); error = true; }
-
- m->gobble(in);
- }
-
- in.close();
-
- if (error) { m->control_pressed = true; }
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "readNames");
- exit(1);
- }
- }
-
-//***************************************************************************************************************
-
-
projects / mothur.git / blobdiff